Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes

The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.

Reconstruction of the ancestral marsupial karyotype from comparative gene maps

BACKGROUND: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n=14 and 2n=22 ancestral marsupial karyotype. RESULTS: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n=14) and therian mammal (2n=19) karyotypes to be reconstructed. CONCLUSIONS: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n=14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

Echolocation calls and wing morphology of bats from the West Indies

Echolocation calls of 119 bats belonging to 12 species in three families from Antillean islands of Puerto Rico, Dominica, and St. Vincent were recorded by using time-expansion methods. Spectrograms of calls and descriptive statistics of five temporal and frequency variables measured from calls are presented. The echolocation calls of many of these species, particularly those in the family Phyllostomidae, have not been described previously. The wing morphology of each taxon is described and related to the structure of its echolocation calls and its foraging ecology. Of slow aerial-hawking insectivores, the Mormoopidae and Natalidae Mormoops blainvillii, Pteronotus davyi davyi, P. quadridens fuliginosus, and Natalus stramineus stramineus can forage with great manoeuvrability in background-cluttered space (close to vegetation), and are able to hover. Pteronotus parnellii portoricensis is able to fly and echolocate in highly-cluttered space (dense vegetation). Among frugivores, nectarivores and omnivores in the family Phyllostomidae, Brachyphylla cavernarum intermedia is adapted to foraging in the edges of vegetation in background-cluttered space, while Erophylla bombifrons bombifrons, Glossophaga longirostris rostrata, Artibeus jamaicensis jamaicensis, A. jamaicensis schwartzi and Stenoderma rufum darioi are adapted to foraging under canopies in highly-cluttered space and do not have speed or efficiency in commuting flight. In contrast, Monophyllus plethodon luciae, Sturnira lilium angeli and S. lilium paulsoni are adapted to fly in highly-cluttered space, but can also fly fast and efficiently in open areas.

A comparison of mark-recapture distance-sampling methods applied to aerial surveys of eastern grey kangaroos

Aerial surveys of kangaroos (Macropus spp.) in Queensland are used to make economically important judgements on the levels of viable commercial harvest. Previous analysis methods for aerial kangaroo surveys have used both mark-recapture methodologies and conventional distance-sampling analyses. Conventional distance sampling has the disadvantage that detection is assumed to be perfect on the transect line, while mark-recapture methods are notoriously sensitive to problems with unmodelled heterogeneity in capture probabilities. We introduce three methodologies for combining together mark-recapture and distance-sampling data, aimed at exploiting the strengths of both methodologies and overcoming the weaknesses. Of these methods, two are based on the assumption of full independence between observers in the mark-recapture component, and this appears to introduce more bias in density estimation than it resolves through allowing uncertain trackline detection. Both of these methods give lower density estimates than conventional distance sampling, indicating a clear failure of the independence assumption. The third method, termed point independence, appears to perform very well, giving credible density estimates and good properties in terms of goodness-of-fit and percentage coefficient of variation. Estimated densities of eastern grey kangaroos range from 21 to 36 individuals km-2, with estimated coefficients of variation between 11% and 14% and estimated trackline detection probabilities primarily between 0.7 and 0.9.

Reassessing spatial and temporal dynamics of kangaroo populations

Long-running datasets from aerial surveys of kangaroos (Macropus giganteus, Macropus [uliginosus, Macropus robustus and Macropus rufus) across Queensland, New South Wales and South Australia have been analysed, seeking better predictors of rates of increase which would allow aerial surveys to be undertaken less frequently than annually. Early models of changes in kangaroo numbers in response to rainfall had shown great promise, but much variability. We used normalised difference vegetation index (NDVI) instead, reasoning that changes in pasture condition would provide a better predictor than rainfall. However, except at a fine scale, NDVI proved no better; although two linked periods of rainfall proved useful predictors of rates of increase, this was only in some areas for some species. The good correlations reported in earlier studies were a consequence of data dominated by large droughtinduced adult mortality, whereas over a longer time frame and where changes between years are less dramatic, juvenile survival has the strongest influence on dynamics. Further, harvesting, density dependence and competition with domestic stock are additional and important influences and it is now clear that kangaroo movement has a greater influence on population dynamics than had been assumed. Accordingly, previous conclusions about kangaroo populations as simple systems driven by rainfall need to be reassessed. Examination of this large dataset has permitted descriptions of shifts in distribution of three species across eastern Australia, changes in dispersion in response to rainfall, and an evaluation of using harvest statistics as an index of density and harvest rate. These results have been combined into a risk assessment and decision theory framework to identify optimal monitoring strategies.

Shedding Light on the Microbial Community of the Macropod Foregut Using 454-Amplicon Pyrosequencing

Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

蝙蝠科三种蝙蝠的G-带和C-带

对肺、心等进行组织培养,用空气干燥法制作染色体标本,对贵州3种蝙蝠即中华鼠耳蝠(Myotischinensis)、西南鼠耳蝠(M.altarium)和亚洲长翼蝠(Miniopterus fuliginosus)进行了G-带、C-带带型分析.结果表明,2种鼠耳蝠的G-带基本相同,亚洲长翼蝠的G-带与两种鼠耳蝠有一定同源性;C-带核型中,中华鼠耳蝠和亚洲长翼蝠只有着丝粒带,而西南鼠耳蝠有的染色体有插入C-带和端位C-带.根据带型异同分析讨论了鼠耳蝠和长翼蝠间的进化关系.

Skull Modularity in Neotropical Marsupials and Monkeys: Size Variation and Evolutionary Constraint and Flexibility

An organism is built through a series of contingent factors, yet it is determined by historical, physical, and developmental constraints. A constraint should not be understood as an absolute obstacle to evolution, as it may also generate new possibilities for evolutionary change. Modularity is, in this context, an important way of organizing biological information and has been recognized as a central concept in evolutionary biology bridging on developmental, genetics, morphological, biochemical, and physiological studies. In this article, we explore how modularity affects the evolution of a complex system in two mammalian lineages by analyzing correlation, variance/covariance, and residual matrices (without size variation). We use the multivariate response to selection equation to simulate the behavior of Eutheria and Metharia skulls in terms of their evolutionary flexibility and constraints. We relate these results to classical approaches based on morphological integration tests based on functional/developmental hypotheses. Eutherians (Neotropical primates) showed smaller magnitudes of integration compared with Metatheria (didelphids) and also skull modules more clearly delimited. Didelphids showed higher magnitudes of integration and their modularity is strongly influenced by within-groups size variation to a degree that evolutionary responses are basically aligned with size variation. Primates still have a good portion of the total variation based on size; however, their enhanced modularization allows a broader spectrum of responses, more similar to the selection gradients applied (enhanced flexibility). Without size variation, both groups become much more similar in terms of modularity patterns and magnitudes and, consequently, in their evolutionary flexibility. J. Exp. Zool. (Mol. Dev. Evol.) 314B:663-683, 2010. (C) 2010 Wiley-Liss, Inc.

Estudo dos restos de peixes dos sítios arqueológicos da área de influência da usina hidrelétrica Machadinho, RS, Brasil

Durante o resgate do material arqueológico dos sítios da região de Piratuba, SC, e de Aratiba, Machadinho e Maximiliano de Almeida, RS, área de influência da Usina Hidroelétrica de Machadinho, foram observadas grandes quantidades de ossos e escamas de peixes incorporando os restos alimentares encontrados nestes locais. Utilizando uma coleção osteológica de referência pudemos identificar restos de Salminus maxillosus Valenciennes, 1850, Brycon orbignyanus (Valenciennes, 1849), Pogonopoma obscurum Quevedo & Reis, 2002, Hemiancistrus fuliginosus Cardoso & Malabarba, 1999, Prochilodus lineatus (Valenciennes, 1836), Schizodon sp., Leporinus sp., Hoplias sp., Hypostomus sp. e Crenicichla sp. Com base em medições realizadas em exemplares de coleções, foram obtidas regressões a partir das dimensões do osso pré-maxilar em Crenicichla spp. e do esporão peitoral em Hemiancistrus fuliginosus, Pogonopoma obscurum e Hypostomus spp. correlacionadas com o comprimento padrão e peso dos espécimes. A partir das estimativas de comprimento padrão e peso das peças ósseas encontradas foi possível formular hipóteses sobre a tecnologia de pesca utilizada pelos habitantes destes sítios.

Comparative cytogenetics of eight species of Cycloramphus (Anura, Cycloramphidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Frugivory on Margaritaria nobilis L.f. (Euphorbiaceae): poor investment and mimetism.

Dehiscent fruits of Euphorbiaceae usually have two stages of seed dispersal, autochory followed by myrmecochory. Two stages of Margaritaria nobilis seed dispersal were described, the first stage autochoric followed by ornithocoric. Their dehiscent fruits are green and after they detached from the tree crown and fall on the ground, they open and expose blue metallic cocas. We studied the seed dispersal system of Margaritaria nobilis in a semi-deciduous forest in Brazil. In 80 h of focal observations, we recorded only 12 visits of frugivores, however the thrush Turdus leucomelas was the only frugivore that swallowed the fruits on the tree crown. Pitylus fuliginosus (Fringilidae) and Pionus maximiliani (Psittacidae) were mainly pulp eaters, dropping the seeds below the tree. on the forest floor, after fruits dehiscence, jays (Cyanocorax chrysops), guans (Penelope superciliaris), doves (Geotrygon montana) and collared-peccaries (Pecari tajacu) were observed eating the blue diaspores of M. nobilis. Experiments in captivity showed that scaly-headed parrots (Pionus maximiliani), toco toucans (Ramphastos toco), jays (Cyanochorax chrysops), and guans (Penelope superciliaris) consumed the fruits and did not prey on the seeds before consumption. The seeds collected from the feces did not germinate in spite of the high viability. The two stages of seed dispersal in M. nobilis resembles the dispersal strategies of some mimetic species. However M. nobilis seeds are associated with an endocarp, it showed low investment in nutrients, and consistent with this hypothesis, M. nobilis shared important characteristics with mimetic fruits, such as bright color display, long seed dormancy and protection by secondary compounds.

Pseudechis australis Venomics: Adaptation for a Defense against Microbial Pathogens and Recruitment of Body Transferrin

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

An Ecological Study of Helminths of Some Wyoming Voles (Microtus spp.) with a Description of a New Species of Nematospiroides (Heligmosomidae: Nematoda)

An ecological and taxonomic study of the helminth parasites of voles (Microtus spp.) in the Jackson Hole region of Wyoming is reported. Nematospiroides microti n. sp. from Microtus montanus nanus and M. richardsoni macropus is described and figured. A cestode, Paranoplocephala infrequens, and a nematode, Syphacia obvelata, were generally distributed throughout the region in all habitats except the sage flats. A trematode, Quinqueserialis hassalli, was recovered only from voles collected near streams at low altitudes. This was presumably due to the localized distribution of the molluscan intermediate host. Four helminths, viz., Hymenolepis horrida, Heligmosomum costellatum, Nematospiroides microti and Trichuris opaca, were restricted in their distribution to the alpine and sub-alpine meadows. Of these parasites, H. horrida and H. costellatum are reported for the first time from North America. Most of the other host and locality records are new. Available data indicate that host specificity was not a factor in restricting the distribution of parasites. Although the greatest numbers of parasites, both qualitative and quantitative, occurred in habitats where host density was greatest, it seems unlikely that host density is the only factor involved.

Guatteria (Annonaceae) da Floresta Atlântica brasileira

Guatteria Ruiz et Pav. é o maior gênero de Annonaceae, com 307 espécies de distribuição neotropical. Caracteres reprodutivos constantes e vegetativos variáveis dificultam a caracterização das espécies. Como resultado do presente estudo são reconhecidas 15 espécies do gênero na Floresta Atlântica, Guatteria australis, G. campestris, G. candolleana, G. emarginata, G. ferruginea, G. latifolia, G. macropus, G. oligocarpa, G. pogonopus, G. pohliana, G. sellowiana, G. schomburgkiana, G. stenocarpa, G. tomentosa e G. villosissima. Oito nomes são sinonimizados e dois lectótipos são indicados. Chave, descrições, comentários taxonômicos, informações sobre fenologia, distribuição geográfica, hábitats de ocorrência, status de conservação e ilustrações são apresentados.